Freesurfer

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30081 discussions

Problem with freesurfer measures
by Alberto Del Cerro Leon 06 Apr '21

06 Apr '21

External Email - Use Caution Hello Freesurfer team, I am using an annotation file that i've created previously to obtain the measures of some ROIs. To do that i am using de commands mri_surf2surf and mri_segstats. I want to obtain the following measures: 1. Gray and White Matter Volume 2. Folding Index 3. Curvature measures 4. Thickness However I don't know what surface in the surf folder of each subject I have to use. Could u help me?

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unsubscribe
by Coleman, Katherine 06 Apr '21

06 Apr '21

Hello, Please remove me from the free surfer forum mailing list. Thank you, Katherine Katherine Coleman, MS Research Assistant II Mood Trajectories and Outcomes Laboratory Department of Psychiatry [cid:image001.jpg@01D6CE33.2A446E30]

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Dicom Tag Problem Reconall
by Banu Femir 06 Apr '21

06 Apr '21

External Email - Use Caution Dear Freesurfer Developers, I'm trying to analyze a set of MRI data that I got via CD. Dicom files did not have .dcm extension, so I used a program and they turned into a .dcm image. My reconall run for around 2 hours, after I got an error: Counting frames nframes = 481 nslices = 1 ndcmfiles = 481 PE Dir = UNKNOWN (dicom read) Loading pixel data JPEG compressed, decompressing cd /home/banu/usr/local/freesurfer/subjects/sepsis1dicomwritebelow fsdcmdecompress --i /home/banu/Documents/Sepsis/yeni_dicom_write_below/F_000001.dcm --o /tmp/banu.tmp.decompressed.dcm.1TXZUy --jpeg >& /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out ERROR: 512, see /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out for more details Linux banuf 4.15.0-51-generic #55-Ubuntu SMP Wed May 15 14:27:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Before that, I got many Warnings about imagenumber, tag serial number, seriesnumber, tag, ect. In case you want I can share the whole log file. I am wondering if there was sth wrong with my .dcm format. If yes, how I can solve this problem? It seems like there was sth wrong with tags, but I really cannot solve the problem. Many thanks! Have a nice and healthy week! Banu

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Re: [Freesurfer] recon-all bug
by zalewk 06 Apr '21

06 Apr '21

External Email - Use Caution Hi freesurfer team, I've tried running recon-all as mentioned before with the -xf flag under different conditions. As far as I can tell, any line using the UpdateNeeded function. e.g.: "set ud = `UpdateNeeded $thickness $pial $white`" fails with the following if statement because the variable $ud includes paths as strings in it instead of a 0/1 integer. Setting it to a 1 or 0 beforehand also seems to solve the problem. The function UpdateNeeded only seems to return an integer as an exit status, so I'm not sure why there are path strings in it causing it to fail. If I print out the $ud variable before it fails and the result is: "/subjectDirectory/subjectID_FREESURFER/mri mri mri_FREESURFER /subjectDirectory/subjectID_FREESURFER/mri/mri_FREESURFER/stats 1" It returns the exit status of 1 preceded by the path of the subject's mri directory, just "mri", "mri_FREESURFER" and the subject's stats directory (all subjects in this particular study have the suffix "_FREESURFER"). It prints this out these strings no matter the variables as .mgz file names, or number of variables passed to the UpdateNeeded function. I still don't have a clue what would cause this behavior. The UpdateNeeded function seems to work fine and as intended as far as I can tell, so I still don't know why these paths/strings are being added and causing it to crash. Best, Kody Zalewski Message: 3 Date: Fri, 02 Apr 2021 03:49:02 +0200 From: fsbuild <fsbuild(a)contbay.com> Subject: Re: [Freesurfer] recon-all bug To: freesurfer(a)nmr.mgh.harvard.edu Cc: cmacd(a)neurosurgery.washington.edu Message-ID: <1617328142.6066780ef2824(a)trashmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Kody, One thing you could try to get more information printed about what is going on is to edit the very first line in the recon-all script to be: #! /bin/tcsh -xf ? instead of #! /bin/tcsh -f Adding the x option will echo each line in the script as it?s run with the variable values expanded, and seeing that output could help with debugging. - R. On Apr 1, 2021, at 20:29, zalewk <zalewk(a)uw.edu> wrote:        External Email - Use Caution        Hi Freesurfer team, My lab recently switched over from FS6 to FS7 and I think I've encountered a bug with recon-all.. I'm running subjects stepwise and editing them, running recon-all with the -autorecon2 and -autorecon3 flags initially are no problem, they run fine.  Trying to re-run them or use the -autorecon2-wm, -autorecon-pial etc. flags lead to crashing at certain parts of the program. The error message I get is "if: expression syntax". Digging into the code, it seems to crash when it hits a line of code "if($ud || $ForceUpdate)". The syntax superficially looks right (I don't know tcsh), checking the variables it seems like $ForceUpdate is never set, but removing it from recon-all doesn't fix the problem.  It seems the $ud variable is for checking if updates are ! needed fo r a set of volumes passed to the program. I don't know why that would be a problematic argument, removing that part seems to fix it, but this also seems like an important variable and I don't know enough about tcsh to understand why it works after removing it. Can one of the folks who wrote the recon-all script help me out? I'm running the commands step-wise as a work-around, but that is much less convenient. Best, Kody Zalewski_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer?

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recon-all bug
by zalewk 06 Apr '21

06 Apr '21

External Email - Use Caution Hi Freesurfer team, My lab recently switched over from FS6 to FS7 and I think I've encountered a bug with recon-all. I'm running subjects stepwise and editing them, running recon-all with the -autorecon2 and -autorecon3 flags initially are no problem, they run fine. Trying to re-run them or use the -autorecon2-wm, -autorecon-pial etc. flags lead to crashing at certain parts of the program. The error message I get is "if: expression syntax". Digging into the code, it seems to crash when it hits a line of code "if($ud || $ForceUpdate)". The syntax superficially looks right (I don't know tcsh), checking the variables it seems like $ForceUpdate is never set, but removing it from recon-all doesn't fix the problem. It seems the $ud variable is for checking if updates are needed for a set of volumes passed to the program. I don't know why that would be a problematic argument, removing that part seems to fix it, but this also seems like an important variable and I don't know enough about tcsh to understand why it works after removing it. Can one of the folks who wrote the recon-all script help me out? I'm running the commands step-wise as a work-around, but that is much less convenient. Best, Kody Zalewski

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retaining label ids
by miracle ozzoude 06 Apr '21

06 Apr '21

External Email - Use Caution Hello Experts, I did like to extract wm whilst retaining the label ids. I tried mri_extract_labels but it didn't work. Any help would be appreciated. Many thanks, Paul

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Regarding recon all
by Amar Shukla 06 Apr '21

06 Apr '21

External Email - Use Caution Dear Team, Actually I am trying to test my own data in recon all , but i have taken only one subject for recon. It shows me this error. ERROR! FOV=408.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** Linux amar-GV62VR-7RF 5.8.0-48-generic #54~20.04.1-Ubuntu SMP Sat Mar 20 13:40:25 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux -- With Regards, Amar Shukla Assistant Professor, M tech AI ANN(2014-2016), Centre Of Information Technology, UPES Contact :+91 897 977 8016

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mri_glmfit error
by Ishi Tandon AIB, Jaipur 06 Apr '21

06 Apr '21

External Email - Use Caution Hello FS experts, I attempted to execute mri_glmfit on my structural data through the following command - mri_glmfit --y final.lh.mTBI.volume.10.mgh --fsgd FSGD/mild.tbi.fsgd dods -C contrats/HC-mTBI.mtx --surf fsaverage --cortex --glmdir lh.volume.glmdir But it gives me an error (attached below) indicating a formatting problem in my FSGD file (attached). I have been trying to figure that out for a while. But I am unable to debug it. Could someone please help me resolve it? Thanks for your time. *Regards,* *Ishi Tandon* *B.Tech + M.Tech - Cognitive Neuroscience* *Amity University, Rajasthan*

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fMRIPrep BOLD Output
by Karan Desai 06 Apr '21

06 Apr '21

External Email - Use Caution Hi Freesurfer List, I am running fMRIPrep and getting the first two FS output files (aseg and aparcaseg seen above in the screenshot), but not the actual file I need which is the one where it is resampled to the mesh. I have run fMRIPrep and have those two files except the actual BOLD series resampled to the surface mesh. Is there a FS command that can be used to do that one step? Best, Karan

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quantification of volume of perivascular spaces
by Antonín Škoch 05 Apr '21

05 Apr '21

External Email - Use Caution Dear experts, We would like to quantify volume of brain perivascular spaces. Ideally longitudinally - i.e. to study the dynamics of perivascular spaces in multiple measurement of the same subject. Is it possible to use samseg for this? Do you think, that --lesion flag in samseg would work estimation of perivascular spaces? Or other setting of samseg will be better option? Or, would you rather recommend other tools? Any idea/comment will be greatly appreciated. Regards, Antonin Skoch

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